The mtDNA sequence of the ostrich and the divergence between paleognathous and neognathous birds

Abstract

The complete mitochondrial DNA (mtDNA) molecule of the ostrich, Struthio camelus, was sequenced. The size of the molecule is 16,591 nucleotides. Since the ostrich represents the paleognathous birds, comparison with the mtDNA of the neognathous chicken, the only avian species reported so far in databases, made it possible to identify common and, probably, general avian mtDNA characteristics. Relative to other vertebrates, the avian NADH6 and tRNA-Glu genes are positioned upstream of the control region rather than the cytochrome b gene. The NADH3 gene of the ostrich is terminated by a stop codon at position 207. Thus, the gene is about 140 nucleotides shorter than in other vertebrates. The sequence for L-strand origin of replication is missing in both birds, and four transfer RNA genes of the two avian mtDNAs deviate from common characteristics of tRNAs of vertebrate mtDNAs by having an adenine (and not a thymidine) at position 8. Due to the absence of suitable fossils, most paleontological datings of avian divergences are conjectural. Molecular dating of the divergence between the ostrich and the chicken indicates that these two avian lineages separated 80-90 MYA. Phylogenetic analysis of complete cytochrome b genes of six avian orders showed that Passeriformes represent the earliest divergence among recent birds, contradicting the commonly accepted notion of a basal position of the Palaeognathae among recent birds.

The Old World Sparrows (Genus Passer) Phylogeography and Their Relative Abundance of Nuclear mtDNA Pseudogenes

“…Also, cranes show a faster rate of nucleotide substitution, closer to our results found in Carduelis, Serinus, and Passer; (about 1%) (Krajewski and King 1996). Notwithstanding, the calculation of species divergence times needs to be confirmed by other methodologies and with additional species in this particular study and others (i.e., Härlid et al 1997). In the later study, Passerines are found to be older than paleognathous birds; also, the relative close-to-Passer Carduelini (Carduelis, Serinus, and others) species are considered nearly as old as Passer (Marten and Johnson 1986;Fehrer 1996;Arnaiz-Villena et al 1998, 1999a, 2001.…”

“…Eight mt cyt b clones were analyzed for each bird and an average of five clones per individual were suitable to be fully analyzed in the automatic sequencer because an average of one to three clones showed PCR mistakes and were discarded. Three different phylogenetic tree-constructing methodologies were used to confirm independently the robustness of the topologies (Härlid et al 1997): unweighted parsimony, neighbor joining (NJ), and unweighted pair group with arithmetic mean (UPGMA). The matrix of genetic distances for the NJ tree was obtained by the maximum-likelihood method, and Kimura two-parameter distances were used for the UPGMA dendrogram.…”

“…On the other hand, it is widely believed that Pleistocene temperature variations (glaciations) and subsequent isolation are the most important factors provoking the appearance of new extant bird species (Gill 1995). Recent contradictory evidence suggests that speciation of some genera and orders may have already occurred a long time ago (Chiappe 1995;Feduccia 1995;Hackett 1996;Hedges et al 1996;Härlid et al 1997), particularly in Passerines (Klicka and Zink 1997) and in Carduelinae (Marten and Johnson 1986;Fehrer 1996;Arnaiz-Villena et al 1998, 1999a. In the present work, we have collected Passer and other related species samples from around the world (Passeridae; Sibley and Monroe 1990) in order to sequence an orthologous gene from each of them: the mt cyt b (924 bp).…”

Sequence variation and structural conservation in the D-loop region and flanking genes of mitochondrial DNA from Japanese pond frogs.

“…Intergeneric, interfamily, and interorder phylogenies have been studied using the 12S and 16S rRNA gene sequences Hay et al, 1995;Titus and Larson, 1995;Ruvinsky and Maxson, 1996;Moore, 1996, 1998;Kobel et al, 1998). On the other hand, the homologies or differences of each mitochondrial gene or D-loop region have been recently reported among several related animal species based on the complete nucleotide sequences of mitochondrial genomes (Giorgi et al, 1996;Lopez et al, 1996;Xu et al, 1996;Härlid et al, 1997;Kim et al, 1998;Sumida et al, in preparation). These studies showed that the degrees of homologies between mtDNAs varied according to the individual genes.…”

Finding function in the unknown

“…These two are quite distant relatives to many bird species (e.g. the molecular divergence between the ostrich and the chicken is approximated at 80-90 MYA [16]). As such, it is not surprising that there is significant variation amongst extant bird species; in fact genome sequencing and transcriptomic studies of some species cannot rely on the available genomes as a reference as they are too divergent.…”